1M5N | pdb_00001m5n

Crystal structure of HEAT repeats (1-11) of importin b bound to the non-classical NLS(67-94) of PTHrP

• PDB DOI: https://doi.org/10.2210/pdb1M5N/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2002-07-09 Released: 2003-01-21 
• Deposition Author(s): Cingolani, G., Bednenko, J., Gillespie, M.T., Gerace, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.297 (Depositor) 
• R-Value Work: 
  0.250 (Depositor) 
• R-Value Observed: 
  0.250 (Depositor) 

Starting Model: experimental

Literature

Molecular basis for the recognition of a nonclassical nuclear localization signal by importin beta

Cingolani, G., Bednenko, J., Gillespie, M.T., Gerace, L.

(2002) Mol Cell 10: 1345-1353

• PubMed: 12504010 
• DOI: https://doi.org/10.1016/s1097-2765(02)00727-x
• Primary Citation Related Structures: 
  1M5N


• PubMed Abstract: 
  

  Nuclear import of proteins containing a classical nuclear localization signal (NLS) involves NLS recognition by importin alpha, which associates with importin beta via the IBB domain. Other proteins, including parathyroid hormone-related protein (PTHrP), are imported into the nucleus by direct interaction with importin beta. We solved the crystal structure of a fragment of importin beta-1 (1-485) bound to the nonclassical NLS of PTHrP. The structure reveals a second extended cargo binding site on importin beta distinct from the IBB domain binding site. Using a permeabilized cell import assay we demonstrate that importin beta (1-485) can import PTHrP-coupled cargo in a Ran-dependent manner. We propose that this region contains a prototypical nuclear import receptor domain, which could have evolved into the modern importin beta superfamily.

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Organizational Affiliation: 
• Departments of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 57.17 kDa 
• Atom Count: 4,020 
• Modeled Residue Count: 513 
• Deposited Residue Count: 513 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Importin beta-1 subunit	A [auth S]	485	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q14974 (Homo sapiens) Explore Q14974  Go to UniProtKB:  Q14974
PHAROS:  Q14974 GTEx:  ENSG00000108424

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Parathyroid hormone-related protein	B [auth Q]	28	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P12272 (Homo sapiens) Explore P12272  Go to UniProtKB:  P12272
PHAROS:  P12272 GTEx:  ENSG00000087494

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.297 (Depositor) 
• R-Value Work:  0.250 (Depositor) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.792	α = 90
b = 105.447	β = 90
c = 146.738	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-21 
Deposition Author(s): Cingolani, G., Bednenko, J., Gillespie, M.T., Gerace, L.

Revision History  

• Version 1.0: 2003-01-21
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Refinement description